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15 protocols using phosphatase and protease inhibitors

1

Western Blot Analysis of Protein Expression

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MH7A cells were seeded in 10 cm culture dishes (430167, Corning, United States) and subjected to the aforementioned treatment. All samples were lysed in RIPA cell lysis buffer (Beyotime, Shanghai, China), containing both phosphatase and protease inhibitors (Roche, Switzerland). Protein concentrations were determined using the BCA Protein Assay Kit (Beyotime, Shanghai, China). Equivalent amounts (70 ug) of each sample was separated by electrophoresis on a 4%–20% SDS-PAGE gel and transferred to PVDF membranes. After blocked with 5% bovine serum albumin for 1 h at room temperature, the membranes were incubation in primary antibody (1:300-1:1000, specific dosage in Supplementary Table S5) overnight at 4°C. The secondary HRP-linked antibody was diluted in 1:5000 (CST) or IRDye secondary antibody was diluted in 1:10000 (LI-COR, United States) and membranes were incubated at room temperature for 1 h. HRP-linked antibody binding was visualized by enhanced chemiluminescence (ECL Prime; Cytiva, China). Blots were imaged using the Odyssey® XF (LICOR, United States) and analysed with ImageJ.
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2

Western Blot Analysis of Proteins

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Total proteins were extracted using RIPA Lysis Buffer supplemented with phosphatase and protease inhibitors (Beyotime). Proteins concentration was quantified using BCA Protein Assay Kit (Beyotime). The protein samples were separated using sodium dodecyl sulphate polyacrylamide gel electrophoresis in 6–12%, and then transferred to a nitrocellulose membrane (Millipore, Billerica, MA, United States). After blocking, the membranes were incubated with primary antibodies at 4°C overnight under shaking conditions. Protein bands were visualised using Tanon 4200 Chemiluminescent Imaging System (Shanghai, China). The relative density of immunoreactive bands was analysed using ImageJ software and β-actin as a loading control. The striping buffer was obtained from Beyotime.
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3

Western Blot Protein Analysis Protocol

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The cells were broken by sonication in RIPA lysis buffer (Beyotime Biotechnology, Shanghai, China) containing phosphatase and protease inhibitors (Beyotime) to extract protein. Protein samples were boiled with 5 × loading buffer (Beyotime). SDS-PAGE gels were used to separate samples, which were then transferred to PVDF membranes. After blocking with 5% skimmed milk and incubating with primary antibodies, the bands were detected using an electrochemiluminescence detection kit (Biosharp, Beijing, China) and captured by chemiluminescence imager (Bio-Rad). The primary antibodies were included in the supplementary file (Additional file 1: Table S2).
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4

Western Blot Analysis of Heart Proteins

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RIPA buffer supplemented with phosphatase and protease inhibitors (Beyotime Biotechnology, China) was used for heart tissues homogenization. Total protein extract (30–50 µg) was loaded to 8–12% SDS-PAGE, transferred onto PVDF membranes, blocked by non-fat dry milk (5%), and then stained with designated primary antibodies: angiotensin II receptor type 1 (AGTR1; Proteintech, 1:1000), cleaved-caspase-3 (Cell Signaling Technology, 1:1000), angiotensin-converting enzyme (ACE; Proteintech, 1:1000), Bcl-2 (Proteintech, 1:1000), Bad (Proteintech, 1:1000), and β-actin (Proteintech, 1:2000) at 4 °C for 24 h. Subsequently, the membranes were rinsed with TBST three times and incubated with goat anti-mouse (Proteintech, 1:1000) or goat anti-rabbit IgG (Proteintech, 1:1000) secondary antibody at ambient temperature for 60 min. The fluorescence signal was visualized by the ChemiDoc™ XRS + imaging system (Bio-Rad, USA) and quantified using Image J (v5.0; National Institutes of Health, USA).
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5

Western Blot Analysis of Signaling Proteins

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Tissues and cells were lysed using RIPA buffer (Cat. No. P0013B, Beyotime, China) supplemented with phosphatase and protease inhibitors (Cat. No. P1005, Beyotime, China). Proteins were quantified using a BCA kit (Cat. No. P0010, Beyotime, China) and then separated by SDS-PAGE (Cat. No. PG113, Epizyme Biomedical Technology Co., China) before being transferred to PVDF membranes (Millipore, USA). These membranes were incubated with primary antibodies against iκB (39 kDa), P65 (65 kDa), P44 (42–44 kDa), P38 (40 kDa), JNK (46–55 kDa) (Cat. No. 9926 T, 8242 T, 4814 T, Cell Signaling Technology, Inc., USA), β-actin (45 kDa), and Lamin-B (67 kDa) (Cat. No. sc-374015, sc-47778, Santa Cruz Biotechnology, Inc., USA), diluted in a 3% bovine serum albumin (BSA) solution at a 1 : 1,000 ratio. Subsequently, they were incubated with the corresponding secondary antibodies. Protein bands were visualized using Super ECL Plus detection reagents (Cat. No. H31500, Tianjin Tiandi Renhe Biotech Co., China) and recorded using a chemiluminescence imaging analysis system (Tanon 5200, YuanPingHao Biotech, China).
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6

Western Blot Analysis of Cell Signaling

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Cells collected by pre-cooled PBS washing were resuspended in cell lysis buffer (Beyotime, China) with phosphatase and protease inhibitors (Beyotime, China). After vortexing and lysing on ice for 10 minutes, protein samples were prepared. Protein concentration was tested using with BCA kit (Beyotime, China). PAGE gels were prepared and loaded with marker and equal amounts of protein samples for separation. Proteins were transferred from gel to PVDF membrane. The membrane was then soaked in 5% skim milk for 60 minutes. After washing with TBST, membrane was incubated with primary antibody at 4°C overnight. Antibodies against Ki-67 were obtained from Huabio (China), and antibodies against IGF1, PARP, Bcl-2, Bax, and cleaved caspase 3 were obtained from ABclonal (China). After washing with TBST, the membrane was incubated with HRP-conjugated goat anti-rabbit IgG secondary antibody for 2 hours at room temperature. Protein bands were assessed using the BeyoECL Plus ultra-sensitive ECL chemiluminescence kit (Beyotime, China).
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7

Western Blot Analysis of Kidney Tissue

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The kidney tissues were homogenized and lysed in RIPA buffer (Beyotime, Nantong, China) with protease inhibitors. The cells were lysed in whole-cell lysate buffer with phosphatase and protease inhibitors (Beyotime). Proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to a polyvinylidene difluoride membrane (Millipore, Boston, MA, USA). The membranes were incubated with primary antibodies including COX-2 (Abcam, Cambridge, UK; dilution 1 : 1000), HistoneH3 (Beyotime; dilution 1 : 1000), β-actin (ProteinTech, Chicago, IL, USA; dilution 1 : 3000), GAPDH (Kangchen, Shanghai, China; dilution 1 : 5000), p-AKT(Ser473), p-AKT(Thr308), p-mTOR(Ser2448), mTOR, GRP78, p-eIF2α, ATF4, CHOP, LC3 and p62 (CST, Danvers, MA, USA; 1 : 1000) overnight at 4 °C, followed by a horseradish peroxidase-conjugated IgG secondary antibody (dilution 1 : 3000) for 1 h at room temperature. Photographs were captured and the relative density of blotting was quantified using Image J software (NIH, Bethesda, MD, USA).
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8

Heatstroke Induction and Dexamethasone Treatment in Mice

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ICR mice were divided into three groups by a computerized randomization procedure. Mice in the Control group were maintained at ambient temperature (23 ± 1 °C). Mice in the Heat group were exposed to an ambient temperature of 41 ± 0.5 °C in a specific environmental control smart chamber (HOPE-MED 8150E, Tianjing, China) until a core temperature of (Tc) > 42.7 °C was achieved (Heatstroke onset). The Heat group animals were then transferred to an ambient temperature of 23 ± 1 °C to recover for 12 h43 (link). Tc was monitored at 15-min intervals using a digital thermometer (ALC-ET06, Shanghai Alcott Biotech Co, Shanghai, China) which was inserted 2 cm into the rectum. Mice in the DEX group were injected intraperitoneally with 25 µg/kg DEX (Selleck; USA) (the Control group was injected with 0.9% saline) immediately after the onset of heatstroke21 (link). Mice were finally anaesthetized with an intraperitoneal injection of sodium pentobarbital (40 mg/kg) and cerebral cortex tissue was harvested from the mice. The tissues were lysed in RIPA lysis buffer (Beyotime Company, Jiangsu, China) containing a cocktail of phosphatase and protease inhibitors (Roche Diagnostics Corp). The supernatant was collected after centrifugation for subsequent protein detection.
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9

Protein Detection in Breast Cancer

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Western blotting was performed using whole-cell lysates of breast cancer cells supplemented with phosphatase and protease inhibitors (Beyotime, Shanghai, China). 20μg proteins were separated by 8–12% SDS-PAGE, transferred onto PVDF membranes (Millipore, Burlington, MA, USA), blocked with 5% BSA (BSA dilution in 1× TBST), and incubated with primary antibodies listed in Table S3 for overnight at 4 °C. Signals from HRP-coupled secondary mouse or rabbit antibodies (Abcam, Cambridge, UK) were generated by Chemiluminescent HRP Substrate (Millipore, Burlington, MA, USA).
The TCA precipitation method was performed to analyze secreted proteins in the conditioned medium as previously described [35 (link)]. 0.5–1 mL conditioned medium was collected and trichloroacetic acid (Macklin, China) was added to a final concentration of 10%, then vortexed for 1min and incubated on ice for 24 h. The samples were centrifuged at 13000 rpm for 20 min at 4 °C, and the supernatant was discarded and washed twice using 100% ice-cold acetone. Subsequently, dried at 37 °C, followed by dissolved in 50 μL 1× loading buffer and heated for 10 min at 95 °C. 10 μL proteins were separated by 10% SDS-PAGE and followed as described above.
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10

Western Blot Analysis of EMT Pathway

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Cells were lysed in RIPA lysis buffer with 1% phosphatase and protease inhibitors (Beyotime, China). Same amount (~20ug) of protein was electrophoresed using 10% SDS-PAGE gel and was transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore, Bedford, MA, USA). The membranes were placed in 5% skimmed milk for 1 h on a rotary shaker to block nonspecific binding sites, followed by incubation with primary specific antibodies overnight at 4°C. On the second day, after washing with 1× TBST buffer three times (10 min/time), anti-mouse or anti-rabbit HRP-labeled secondary antibodies were added and incubated at room temperature for 1 h. After washing again, the membranes were subjected to immunoblotting analysis using ECL detection reagent (Beyotime, China). The primary antibodies used in this study were as follows: PTBP3 (#sc-100845, Santa Cruz Biotechnology), EMT antibody sampler kit (#9782, CST), Smad2/3 antibody sampler kit (#12747, CST), PAI-1 (#11907, CST), TβRI (#sc-101574, Santa Cruz Biotechnology), TβRII (#sc-17791, Santa Cruz Biotechnology), Akt (#4691, CST), p-Akt (#4060, CST), MEK (#4694, CST), p-MEK (#9154, CST), Erk (#12950, CST), and p-Erk (#4370, CST).
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